Rather, the problem is when you hover over it. On Meta, if you hover over the flag so it turns from white to black, the heights of the two images are not the same. It results in the control (and anything below it) being shifted up one pixel if the comment's length is short and does not increase the height.

It's different on Programmers. On Programmers, the height and width are off. See Does tweeting 9 to 5 hurt job applicants? for an example. (Specifically, GrandMasterB's comment on the original question post)

Due to the way browsers render font sizes and line lengths, this may vary.

However, there is an extremely simple way to know something is wrong: the bottom of the hovered "flag" image is cut off.

Here is a short comment (hover over the flag!) to demonstrate.
– CoreyFeb 11 '11 at 3:14

Here is a relatively long comment so you can see the different effects the incorrect image sizes have on the alignment of comments. I'm probably looking too deeply into this, as I imagine it's just a simple fluke with the CSS rules that splice the main sprite image, and that Jin can fix it in about 5 seconds.
– CoreyFeb 11 '11 at 3:16